Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate WP_022947281.1 H035_RS0101685 aspartate kinase
Query= BRENDA::O69077 (412 letters) >NCBI__GCF_000421465.1:WP_022947281.1 Length = 408 Score = 564 bits (1454), Expect = e-165 Identities = 293/409 (71%), Positives = 344/409 (84%), Gaps = 3/409 (0%) Query: 1 MALIVQKFGGTSVGTVERIEQVAEKVKKFREAGDDVVVVVSAMSGETNRLIGLANQIMEQ 60 MAL V K+GGTSVGTVERI+ VAEK+ + + AGDD+VVVVSAMSGET+RL+GLA+Q+ E+ Sbjct: 1 MALYVHKYGGTSVGTVERIQDVAEKIIQAKRAGDDLVVVVSAMSGETDRLLGLAHQVQER 60 Query: 61 PVPRELDVMVSTGEQVTIALLSMALIKRGVPAVSYTGNQVRILTDSAHTKARILHIDDTH 120 P PRELDV+++TGEQVTIALL MAL +G A SYTG Q RILTD+AHTKARIL ID + Sbjct: 61 PEPRELDVLLATGEQVTIALLCMALEVKGCAASSYTGAQARILTDAAHTKARILDIDTSR 120 Query: 121 IRADLKAGRVVVVAGFQGVDGNGNITTLGRGGSDTTGVALAAALKADECQIYTDVDGVYT 180 IR DL +VVVVAGFQGV+ G+ITTLGRGGSDTT VALAA L+ADEC+IYTDVDGVYT Sbjct: 121 IRRDLSQDKVVVVAGFQGVNEEGHITTLGRGGSDTTAVALAATLQADECRIYTDVDGVYT 180 Query: 181 TDPRVVPQARRLDKITFEEMLEMASLGSKVLQIRAVEFAGKYNVPLRVLHSFQEGPGTLI 240 TDPR+ +ARRL++ITFEEMLE+ASLGSKVLQIRAVEFAGKYNVPLRVL +F EG GTLI Sbjct: 181 TDPRIESKARRLERITFEEMLELASLGSKVLQIRAVEFAGKYNVPLRVLSTFTEGEGTLI 240 Query: 241 TIDDEEESMEQPIISGIAFNRDEAKLTIRGVPDTPGVAFKILGPISAANVEVDMIVQNVA 300 T +D E+ME+ +ISGIAFNRDEAKLT+ GVPD PG+A ILGPI+ AN+EVDMIVQNVA Sbjct: 241 TYED--ETMEEALISGIAFNRDEAKLTVEGVPDRPGIAAAILGPIADANIEVDMIVQNVA 298 Query: 301 HDNTTDFTFTVHRNDYLNALEILKQTAANIGAREAIGDTNIAKVSIVGVGMRSHAGVASR 360 D +TDFTFTVHRNDY A +IL + ++GAR+ GD I K+S+VGVGMRSHAG+AS+ Sbjct: 299 EDESTDFTFTVHRNDYPRARDILDRARDDLGARKVTGDDRIVKISLVGVGMRSHAGIASK 358 Query: 361 MFEALAKESINIQMISTSEIKVSVVIEEKYLELAVRALHTAFELD-APA 408 MF LA+ INIQMISTSEIK+SVV++E YL+ AV LH AFELD APA Sbjct: 359 MFRVLAEAGINIQMISTSEIKISVVLDEDYLQAAVHTLHEAFELDQAPA 407 Lambda K H 0.317 0.133 0.362 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 555 Number of extensions: 16 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 412 Length of database: 408 Length adjustment: 31 Effective length of query: 381 Effective length of database: 377 Effective search space: 143637 Effective search space used: 143637 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_022947281.1 H035_RS0101685 (aspartate kinase)
to HMM TIGR00657 (aspartate kinase (EC 2.7.2.4))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR00657.hmm # target sequence database: /tmp/gapView.17759.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00657 [M=442] Accession: TIGR00657 Description: asp_kinases: aspartate kinase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-141 458.7 6.6 1.7e-138 448.4 6.6 2.0 1 lcl|NCBI__GCF_000421465.1:WP_022947281.1 H035_RS0101685 aspartate kinase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000421465.1:WP_022947281.1 H035_RS0101685 aspartate kinase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 448.4 6.6 1.7e-138 1.7e-138 1 441 [. 1 401 [. 1 402 [. 0.98 Alignments for each domain: == domain 1 score: 448.4 bits; conditional E-value: 1.7e-138 TIGR00657 1 maliVqKFGGtSvgnverikkvakivkkekekgnqvvVVvSAmagvTdaLvelaekvsseeekelieki 69 mal V K+GGtSvg+veri++va+ ++++k+ g++ vVVvSAm+g Td+L+ la++v++++ lcl|NCBI__GCF_000421465.1:WP_022947281.1 1 MALYVHKYGGTSVGTVERIQDVAEKIIQAKRAGDDLVVVVSAMSGETDRLLGLAHQVQERP-------- 61 6788*********************************************************........ PP TIGR00657 70 rekhlealeelasqalkeklkallekeleevkkereldlilsvGEklSaallaaaleelgvkavsllga 138 + +reld++l++GE++++all++ale +g+ a s++ga lcl|NCBI__GCF_000421465.1:WP_022947281.1 62 ------------E--------------------PRELDVLLATGEQVTIALLCMALEVKGCAASSYTGA 98 ............3....................8*********************************** PP TIGR00657 139 eagiltdsefgrAkvleeikterleklleegiivvvaGFiGatekgeittLGRGGSDltAallAaalkA 207 +a iltd+++++A+ + +i+t+r+ l+++++vvvaGF+G++e+g+ittLGRGGSD+tA++lAa l+A lcl|NCBI__GCF_000421465.1:WP_022947281.1 99 QARILTDAAHTKAR-ILDIDTSRIRRDLSQDKVVVVAGFQGVNEEGHITTLGRGGSDTTAVALAATLQA 166 **************.****************************************************** PP TIGR00657 208 deveiytDVdGiytaDPrivpeArrldeisyeEalELaslGakvLhprtlepamrakipivvkstfnpe 276 de++iytDVdG+yt+DPri ++Arrl+ i++eE+lELaslG+kvL+ r++e+a ++++p++v stf + lcl|NCBI__GCF_000421465.1:WP_022947281.1 167 DECRIYTDVDGVYTTDPRIESKARRLERITFEEMLELASLGSKVLQIRAVEFAGKYNVPLRVLSTFTEG 235 ******************************************************************998 PP TIGR00657 277 aeGTlivakskseeepavkalsldknqalvsvsgttmkpgilaevfgalaeakvnvdlilqsssets.. 343 eGTli+ +++ +ee ++++++++++a+++v+g++++pgi+a ++g +a+a+++vd+i+q++ e+ lcl|NCBI__GCF_000421465.1:WP_022947281.1 236 -EGTLITYEDETMEEALISGIAFNRDEAKLTVEGVPDRPGIAAAILGPIADANIEVDMIVQNVAEDEst 303 .**************************************************************954446 PP TIGR00657 344 .isfvvdkedadkakellkkkvkeekaleevevekklalvslvGagmksapgvaakifeaLaeeninie 411 +f+v+++d+++a +l+ ++++ ++v+ ++++ ++slvG gm+s+ g+a+k+f +Lae++ini+ lcl|NCBI__GCF_000421465.1:WP_022947281.1 304 dFTFTVHRNDYPRARDILD-RARDDLGARKVTGDDRIVKISLVGVGMRSHAGIASKMFRVLAEAGINIQ 371 8****************95.6899999999*************************************** PP TIGR00657 412 missseikisvvvdekdaekavealheklv 441 mis+seikisvv de++ ++av++lhe+++ lcl|NCBI__GCF_000421465.1:WP_022947281.1 372 MISTSEIKISVVLDEDYLQAAVHTLHEAFE 401 ***************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (442 nodes) Target sequences: 1 (408 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.05u 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 3.15 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory